Atlantic salmon from large Scottish east coast rivers - genetic stock identification: report

References

Anderson, E. C. 2017. Rubias-genetic stock identification (GSI) in the tidyverse. https://github.com/eriqande/rubias

Armstrong, J. D., Gauld, N. R., Gilbey, J., & Morris, D. J. 2018. Application of acoustic tagging, satellite tracking and genetics to assess the mixed stock nature of coastal net fisheries. Scottish Marine and Freshwater Science, 9,27pp.

Beacham, T.D., Wallace, C.G., Jonsen, K., McIntosh, B., Candy, J.R., Horst, K., Lynch, C., Willis, D., Luedke, W., Kearey, L. & Rondeau, E.B. 2021. Parentage‐based tagging combined with genetic stock identification is a cost‐effective and viable replacement for coded‐wire tagging in large‐scale assessments of marine Chinook salmon fisheries in British Columbia, Canada. Evolutionary Applications, 14, 1365-1389.

Begg, G.A., Friedland, K.D. & Pearce, J.B. 1999. Stock identification and its role in stock assessment and fisheries management: an overview. Fisheries Research, 43, 1-8.

Benjamini, Y. & Hochberg, Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B (Methodological), 57, 289-300.

Bradbury, I.R., Wringe, B.F., Watson, B., Paterson, I., Horne, J., Beiko, R., Lehnert, S.J., Clément, M., Anderson, E.C., Jeffery, N.W., Duffy, S., Sylvester, E., Roberston, M. & Bentzen, P. 2018. Genotyping‐by‐sequencing of genome‐wide microsatellite loci reveals fine‐scale harvest composition in a coastal Atlantic salmon fishery. Evolutionary Applications, 11, 918-930.

Cauwelier, E., Gilbey, J. & Middlemas, S. 2016. Genetic assignment of marine-caught adult salmon at Armadale to region of origin. Aberdeen, Scotland, U.K. Scottish Marine and Freshwater Science Report 6/16. 19 pp.

Cauwelier, E., Gilbey, J., Sampayo, J., Stradmeyer, L. & Middlemas, S.J. 2018b. Identification of a single genomic region associated with seasonal river return timing in adult Scottish Atlantic salmon (Salmo salar), using a genome-wide association study. Canadian Journal of Fisheries and Aquatic Sciences, 75, 1427-1435.

Cauwelier, E., Stewart, D.C., Millar, C.P., Gilbey, J., & Middlemas, S.J. 2018a. Across rather than between river genetic structure in Atlantic salmon Salmo salar in north‐east Scotland, UK: Potential causes and management implications. Journal of Fish Biology, 92, 607-620.

Davidsen, J.G., Rikardsen, A. H., Halttunen, E., Thorstad, E.B., Økland, F., Letcher, B.H., Skarðhamar, T. & Næsje, T.F. 2009. Migratory behaviour and survival rates of wild northern Atlantic salmon Salmo salar post‐smolts: effects of environmental factors. Journal of Fish Biology, 75, 1700-1718.

Earl, D.A. & vonHoldt, B.M. 2011. Structure Harvester: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 3, 429-431.

Evanno, G., Regnaut, S. & Goudet, J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14, 2611-2620.

Falush, D., Stephens, M. & Pritchard, J. K. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164, 1567-1587.

Friedland, K.D. 1998. Ocean climate influences on critical Atlantic salmon (Salmo salar) life history events. Canadian Journal of Fisheries and Aquatic Sciences, 55, 119-130.

Fuentes-Pardo, A.P., Pettersson, M., Sprehn, C. G., Andersson, L. & Farrell, E. 2020. Population structure of the Atlantic horse mackerel (Trachurus trachurus) revealed by whole-genome sequencing. A report prepared for the members of the Northern Pelagic Working Group and the Pelagic Advisory Council. 38pp.

Gilbey, J., Knox, D., O'Sullivan, M. & Verspoor, E. 2005. Novel DNA markers for rapid, accurate, and cost-effective discrimination of the continental origin of Atlantic salmon (Salmo salar L.). ICES Journal of Marine Science, 62, 1606-1616.

Gilbey, J., Cauwelier, E., Coulson, M.W., Stradmeyer, L., Sampayo, J.N., Armstrong, A., Verspoor, E., Corrigan, L., Shelley, J. & Middlemas, S. 2016a. Accuracy of assignment of Atlantic salmon (Salmo salar L.) to rivers and regions in Scotland and northeast England based on single nucleotide polymorphism (SNP) markers. PLoS One, 11, e0164327.

Gilbey, J., Cauwelier, E., Stradmeyer, L., Sampayo, J., Middlemas, S., Corrigan, L., and Shelly, J. 2016b. Assignment of fish from the north east English net fishery to origin using SNP genetic markers. Marine Scotland Science and the Environment Agency Report. Faskally, Pitlochry, Scotland. U.K. 45pp.

Gilbey, J., Coughlan, J., Wennevik, V., Prodöhl, P., Stevens, J. R., Garcia de Leaniz, C., Ensing, D., Cauwelier, E., Cherbonnel, C., Consuegra, S., Coulson, M.W., Cross, T.F., Crozier, W., Dillane, E., Ellis, J.S., García-Vázquez, E., Griffiths, A., Gudjonsson, S., Hindar, K., Karlsson, S., Knox, D., Machado-Schiaffino, G., Meldrup, D., Nielsen, E.G., Ólafsson, K., Primmer, C.R., Prusov, S., Stradmeyer, L., Vähä, J.-P., Veselov, A.J., Webster, L,M.I., McGinnity, P. & Verspoor, E. 2018. A microsatellite baseline for genetic stock identification of European Atlantic salmon (Salmo salar L.). ICES Journal of Marine Science, 75, 662-674.

Gilbey, J., Utne, K. R., Wennevik, V., Beck, A. C., Kausrud, K., Hindar, K., Garcia de Leaniz, C., Cherbonnel, C., Coughlan, J., Cross, T.F., Dillane, E., Ensing, D., García-Vázquez, E., Hole, L.R., Holm, M., Holst, J.C., Jacobsen, J.A., Jensen, A.J., Karlsson, S., Ó Maoiléidigh, N., Mork, K.A., Nielsen, E.E., Nøttestad, L., Primmer, C.R., Prodöhl, P., Prusov, S., Stevens, J.R., Thomas, K., Whelan, K., McGinnity, P. & Verspoor, E. 2021. The early marine distribution of Atlantic salmon in the North‐east Atlantic: A genetically informed stock‐specific synthesis. Fish and Fisheries, 22, 1274-1306.

Griffiths, A.M., Machado-Schiaffino, G., Dillane, E., Coughlan, J., Horreo, J.L., Bowkett, A. E., Minting, P., Toms, S., Roche, W., Gargan, P., McGinnity, P., Cross, T., Bright, D., García-Vázquez, E. & Stevens, J.R. 2010. Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range. BMC Genetics, 11, 1-27.

Griffiths, A.M., Ellis, J.S., Clifton-Dey, D., Machado-Schiaffino, G., Bright, D., Garcia-Vazquez, E. & Stevens, J.R. 2011. Restoration versus recolonisation: The origin of Atlantic salmon (Salmo salar L.) currently in the River Thames. Biological Conservation, 144, 2733-2738.

Hansen, M.M., Nielsen, E.E. & Mensberg, K.L.(1997. The problem of sampling families rather than populations: relatedness among individuals in samples of juvenile brown trout Salmo trutta L. Molecular Ecology, 6, 469-474.

Jakobsson, M. & Rosenberg, N.A. 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23, 1801-1806.

Jones, O.R. & Wang, J. 2010. COLONY: a program for parentage and sibship inference from multilocus genotype data. Molecular Ecology Resources, 10, 551-555.

Kalinowski, S.T. 2005. hp‐rare 1.0: a computer program for performing rarefaction on measures of allelic richness. Molecular Ecology Notes, 5, 187-189.

Koljonen, M.L. & McKinnell, S. 1996. Assessing seasonal changes in stock composition of Atlantic salmon catches in the Baltic Sea with genetic stock identification. Journal of Fish Biology, 49, 998-1018.

Larson, W.A., Seeb, L.W., Everett, M.V., Waples, R.K., Templin, W.D. & Seeb, J. E. 2014. Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha). Evolutionary Applications, 7, 355-369.

Malcolm, I. A., Millidine, K. J., Jackson, F.L., Glover, R.S. & Fryer, R.J. (2020). The National Electrofishing Programme for Scotland (NEPS) 2019. Scottish Marine and Freshwater Science, 11/9. 57pp.

Marine Scotland Science 2020 rod catch returns data: https://data.marine.gov.scot/dataset/salmon-and-sea-trout-fishery-statistics-2020-season-reported-catch

Marklevitz, S.A., Fryer, B.J., Gonder, D., Yang, Z., Johnson, J., Moerke, A. & Morbey, Y.E., 2011. Use of otolith chemistry to discriminate juvenile Chinook salmon (Oncorhynchus tshawytscha) from different wild populations and hatcheries in Lake Huron. Journal of Great Lakes Research, 37, pp.698-706.

Moriya, S., Sato, S., Azumaya, T., Suzuki, O., Urawa, S., Urano, A. & Abe, S. 2007. Genetic stock identification of chum salmon in the Bering Sea and North Pacific Ocean using mitochondrial DNA microarray. Marine Biotechnology, 9, 179-191.

Narum, S.R., Di Genova, A., Micheletti, S.J. & Maass, A. 2018. Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon. Proceedings of the Royal Society B: Biological Sciences, 285, 20180935.

Nei, M., Tajima, F. & Tateno, Y. 1983. Accuracy of estimated phylogenetic trees from molecular data. Journal of Molecular Evolution, 19, 153-170.

Peakall, R.O.D. & Smouse, P.E. 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288-295.

Perrier, C., Daverat, F., Evanno, G., Pécheyran, C., Bagliniere, J.L. & Roussel, J.M. 2011. Coupling genetic and otolith trace element analyses to identify river-born fish with hatchery pedigrees in stocked Atlantic salmon (Salmo salar) populations. Canadian Journal of Fisheries and Aquatic Sciences, 68, pp.977-987.

Potter E.C.E., & Crozier, W.W. 2000. A perspective on the marine survival of Atlantic salmon. In: Mills, D., ed. The Ocean Life of Atlantic salmon: Environmental and Biological Factors Influencing Survival. Oxford: Fishing News Books, Blackwell Science, 19–36.

Pritchard, J.K., Wen, W. & Falush, D. 2004. Documentation for STRUCTURE software: ver. 2.3.

Pritchard, J.K., Stephens, M. & Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.

Ramsay, A.L., Milner, N. J., Hughes, R.N. & McCarthy, I.D. 2011. Comparison of the performance of scale and otolith microchemistry as fisheries research tools in a small upland catchment. Canadian Journal of Fisheries and Aquatic Sciences, 68, 823-833.

R Core Team. 2015. R: A language and environment for statistical computing. R Foundation for Statistical Computing. http://www.R-project.org.

Rosenberg, N.A. 2004. DISTRUCT: a program for the graphical display of population structure. Molecular Ecology Notes, 4, 137-138.

Rousset, F. 2008. GENEPOP’007: a complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources, 8 103-106.

Shaklee, J.B., Beacham, T.D., Seeb, L. & White, B.A. 1999. Managing fisheries using genetic data: case studies from four species of Pacific salmon. Fisheries Research, 43, 45-78.

Sylvester, E.V.A., Beiko, R.G., Bentzen, P., Paterson, I., Horne, J.B., Watson, B., Lehnert, S., Duffy, S., Clément, M., Robertson, M.J. & Bradbury, I.R. 2018. Environmental extremes drive population structure at the northern range limit of Atlantic salmon in North America. Molecular Ecology, 27, 4026-4040.

Thorstad, E.B., Whoriskey, F., Rikardsen, A.H. & Aarestrup, K. 2011. Aquatic Nomads: The Life and Migrations of the Atlantic Salmon. In: Aas, O., Einum, S., Klemetsen, A. & Skurdal, J. eds. Atlantic Salmon Ecology. Wiley-Blackwell. 1–32.

Vähä, J. P., Erkinaro, J., Niemelä, E., Primmer, C. R., Saloniemi, I., Johansen, M., Svenning, M. & Brørs, S. 2011. Temporally stable population‐specific differences in run timing of one‐sea‐winter Atlantic salmon returning to a large river system. Evolutionary Applications, 4, 39-53.

Veinott, G. & Porter, R. 2005. Using otolith microchemistry to distinguish Atlantic salmon (Salmo salar) parr from different natal streams. Fisheries Research, 71, pp.349-355.

Veinott, G., Westley, P.A., Warner, L. & Purchase, C.F. 2012. Assigning origins in a potentially mixed‐stock recreational sea trout (Salmo trutta) fishery. Ecology of Freshwater Fish, 21, 541-551.

Walsh, P.S., Metzger, D.A. & Higuchi, R. 1991. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques, 10, 506-513.

Waples, R.S., Winans, G.A., Utter, F.M. & Mahnken, C. 1990. Genetic approaches to the management of Pacific salmon. Fisheries, 15, 19-25.

Waples, R.S., Dickhoff, W.W., Hauser, L. & Ryman, N. 2008. Six decades of fishery genetics: taking stock. Fisheries, 33, 76-79.

Zhan, L., Paterson, I.G., Fraser, B.A., Watson, B., Bradbury, I.R., Nadukkalam Ravindran, P., Reznick, D., Beiko, R.G. & Bentzen, P. 2017. MEGASAT: automated inference of microsatellite genotypes from sequence data. Molecular Ecology Resources, 17, 247-256.